All,
In the past days, the bug fixed itself. All thumbnail including the older ones, the ones confirmed as affected, and ones of file added later, are displaying correctly.
I can confirm this is not because of an update from Directory Opus. I just saw the 13.16 version today which is why I am rechecking this issue. I've checked the other software updates from the past few days, so a few things I could exclude - Windows Update as none is applied on my system since June 2nd; my codec package is updated in May; and Dropbox last update is in May.
I do suspect this is related to old Windows Media Player, which I've uninstalled from Windows features last Friday. I was not expecting this would change anything, but it is likely the cause.
Anyways, thank you all for attention and helps. If any future user got into the same issue, you could try remove Windows Media Player.